The invention discloses a PCI (Peripheral Component Interconnect) bus controller and a control method thereof. Through SPI (Serial Peripheral Interface) signal multiplexing, two configuration information initialization ways including EEPROM (Electrically Erasable Programmable Read-Only Memory) loading or unloading are provided so as to be flexible in use; and through the arrangement of a plurality of interface modules, a SPI bus, a PCI bus, a Local bus and corresponding pin interfaces can be realized. The PCI bus controller can be used as PCI master/slave equipment, has a wide application range and meets different requirements of a system; and when the PCI bus controller is used as the PCI master equipment, DMA (Direct Memory Access) data transmission is carried out, CPU (Central Processing Unit) intervention is avoided, and system efficiency is improved. When the PCI bus controller is used as the PCI bus master equipment to initiate a bus operation, data interaction between system memory and Local equipment is finished; and during non DMA transmission, the PCI bus controller is used as the PCI bus slave equipment to response to the bus operation. The PCI bus controller provides 8-bit, 16-bit, 32-bit multiplex/non-multiplex Local bus interfaces, can configure and realize various working ways including emergency, prefetching, internal waiting, external waiting, write cycle maintaining, read-write gating delay, big end and small end alignment, local chip selection, local interruption and the like, and is high in universality.